[Dock-fans] Fwd: Re: Parallel install

Scott Brozell sbrozell at scripps.edu
Wed Sep 26 10:25:08 PDT 2007


Hi,

On Wed, 26 Sep 2007, Francesco Pietra wrote:

> The whole thread is below for record, though, new events are all summarized
> here.
>
> There are two compilations, dock6 and dock6.mpi, in:
>
> /usr/local/dock6/bin
>
> I stick at
>
> MPICH_HOME=/usr/local
>
> Then I delete the outputs of previous "make test" and carry out new ones as
> follows
>
> (1) From the directory
> /usr/local/dock6/install
>
> make clean
> make test | tee test.out
>
> (2) From the directory
>
> /usr/local/dock6/install/test
>
> make check | tee check.out
>
> The two output files are attached. Again, test.out is very short and looks very
> similar to previous trials. I am quite sorry to give these troubles.


The tests are failing as before.  The error message is not being
redirected.  Watch the actual full output as it is emitted or
use the correct syntax to pipe stderr (for bash):

make test 2>&1 | tee test.out

Scott

> --- Scott Brozell <sbrozell at scripps.edu> wrote:
>
> > Hi,
> >
> > On Wed, 26 Sep 2007, Francesco Pietra wrote:
> >
> > > Please see below the results of the commands suggested.
> > >
> > > --- Scott Brozell <sbrozell at scripps.edu> wrote:
> > >
> > > > On Tue, 25 Sep 2007, Francesco Pietra wrote:
> > > >
> > > > > I forgot to add the config.h. Attached now
> > > > >
> > > > > --- Francesco Pietra <chiendarret at yahoo.com> wrote:
> > > > >
> > > > > > Date: Tue, 25 Sep 2007 08:25:35 -0700 (PDT)
> > > > > > From: Francesco Pietra <chiendarret at yahoo.com>
> > > > > > Subject: Re: [Dock-fans] Parallel install
> > > > > > To: Sudipto Mukherjee <sudmukh at yahoo.com>, dock-fans
> > > > <dock-fans at docking.org>
> > > > > >
> > > > > > Dear Sudipto:
> > > > > >
> > > > > > Thanks. I fear that something was wrong with my installation of
> > dock6.1.
> > > > > >
> > > > > > Leaving config.h as it was in my previous mail (attached here again)
> > I
> > > > did:
> > > > > >
> > > > > > (1) set the env var (bash)
> > > > > > MPICH_HOME=/usr/local
> > > >
> > > > This is unlikely to be the correct path.
> > >
> > > > Try the command:
> > > > which mpicxx
> > > > and the use the part before bin.
> > >
> > > which mpicxx
> > > /usr/local/bin/mpicxx
> > >
> > >
> > > > Or try the command
> > > > locate mpi.h
> > >
> > >
> > > # updatedb
> > > $ locate mpi.h
> > >
> > > /usr/include/sc/util/group/memmtmpi.h
> > > /usr/include/sc/util/group/messmpi.h
> > > /usr/local/dock6/src/dock/base_mpi.h
> > > /usr/local/include/mpi.h
> > > /usr/local/openmpi-1.2.3/ompi/include/mpi.h
> > > /usr/local/openmpi-1.2.3/ompi/include/mpi.h.in
> > > /usr/local/openmpi-1.2.3/ompi/mpi/f77/prototypes_mpi.h
> > >
> > >
> > > On these basis, having previously set
> > >
> > > MPICH_HOME=/usr/local
> > >
> > > should I proceed to the next suggestions for env variable, or should I
> > first
> > > remove the above one?
> >
> > Based on that info either
> > MPICH_HOME=/usr/local
> > or
> > MPICH_HOME=/usr/local/openmpi-1.2.3/ompi
> > are probably correct.
> >
> > Scott
> >
> > > Thanks
> > > francesco
> > >
> > >
> > >
> > >
> > > > Also use the command export:
> > > > MPICH_HOME=/bla
> > > > export MPICH_HOME
> > > >
> > > > > > (the daemons of openmpi are in /usr/local/bin, which is on my PATH)
> > > > > >
> > > > > > (2) make dock # builds only the dock program
> > > > > >
> > > > > > (the attached test_parallel_onlydock.out reports the "make test")
> > > > > >
> > > > > >
> > > > > > (3) make utils # builds only the accessory programs
> > > > > >
> > > > > > (the attached test_parallel_dockandaccessory.out reports the "make
> > test")
> > > > > >
> > > > > > Attached is also test_serial.out from the "make test" for the serial
> > > > > > installation.
> > > >
> > > > Yes, something is wrong; test_serial.out appears to be truncated
> > > > as do the others; this is the tail:
> > > > make[2]: Leaving directory
> > `/usr/local/dock6/install/test/anchor_and_grow'
> > > > cd bump_filter && make test
> > > > make[2]: Entering directory `/usr/local/dock6/install/test/bump_filter'
> > > > cd ../grid_generation && make test
> > > > make[3]: Entering directory
> > `/usr/local/dock6/install/test/grid_generation'
> > > > # Construct box to enclose spheres
> > > > ../../../bin/showbox < box.in > /dev/null
> > > > make[3]: Leaving directory
> > `/usr/local/dock6/install/test/grid_generation'
> > > > make[2]: Leaving directory `/usr/local/dock6/install/test/bump_filter'
> > > > make[1]: Leaving directory `/usr/local/dock6/install/test'
> > > >
> > > >
> > > > Retry the tests, reporting the verbatim output via:
> > > > cd install;make test
> > > >
> > > > Scott
> > > >
> > > > > > In all case the "make test" was extremely short.
> > > > > >
> > > > > > The system is amd64opteron Debian Linux amd64 etch.
> > > > > >
> > > > > > Thanks for any advice
> > > > > >
> > > > > > francesco
> > > > > >
> > > > > >
> > > > > >
> > > > > > --- Sudipto Mukherjee <sudmukh at yahoo.com> wrote:
> > > > > >
> > > > > > > Dear Francesco,
> > > > > > >
> > > > > > > MPICH_HOME needs to be set as an environment variable.
> > > > > > > You should not have to make any modifications to config.h
> > > > > > > For example, if your login shell is csh, add the following to your
> > > > .cshrc
> > > > > > > setenv MPICH_HOME      /path/to/openmpi
> > > > > > >
> > > > > > > Please also note that MPICH_HOME needs to be the root of the MPI
> > > > > > installation
> > > > > > > folder.
> > > > > > > In your case, this is most likely /usr/local/openmpi or similar.
> > > > > > >
> > > > > > > Regards
> > > > > > > Sudipto Mukherjee
> > > > > > > Graduate Student, Robert C. Rizzo Lab
> > > > > > > Dept. of Applied Math & Statistics, Stony Brook University
> > > > > > > Lab: 631-632-8519, Mobile: 631-220-5744
> > > > > > >
> > > > > > >
> > > > > > > ----- Original Message ----
> > > > > > > From: Francesco Pietra <chiendarret at yahoo.com>
> > > > > > > To: dock-fans <dock-fans at docking.org>
> > > > > > > Sent: Friday, September 21, 2007 5:14:56 PM
> > > > > > > Subject: [Dock-fans] Parallel install
> > > > > > >
> > > > > > > On a shared memory computer with two dual-opterons, OS Linux Debian
> > > > amd64
> > > > > > > etch,
> > > > > > > I have successfully installed
> > > > > > >
> > > > > > > /usr/local/dock6
> > > > > > >
> > > > > > > serial dock and accessory (DOCK 6.1) with g++ 4.1.2, gcc 3.4, g77
> > 3.4.
> > > > > > >
> > > > > > > On this computer, Amber9 is installed in /usr/local/amber9 with
> > openmpi
> > > > > > > support
> > > > > > >
> > > > > > > MPI_HOME=/usr/local
> > > > > > >
> > > > > > > where openmpi is compiled with Intel.
> > > > > > >
> > > > > > > I would be very grateful for suggesting me how to rearrange the
> > > > config.h
> > > > > > file
> > > > > > > (please, see below) so that  MPICH_HOME points to openmpi:
> > > > > > >
> > > > > > > # DOCK configuration file for GNU compilers with MPICH2 based
> > > > parallelism.
> > > > > > > # This configuration file can be used on many platforms:
> > > > > > > #  Linux, Macintosh OS X, Windows with Cygwin, etc.
> > > > > > > # If g77 is not available then change FC below to gfortran or g95.
> > > > > > >
> > > > > > > # REQUIREMENTS - define these environment variables:
> > > > > > > # MPICH_HOME is the root directory of the MPICH2 MPI implementation
> > > > > > > # END REQUIREMENTS
> > > > > > >
> > > > > > > # TROUBLESHOOTING
> > > > > > > # 1. Linking problems, such as undefined references, cannot find
> > > > -lbla_bla,
> > > > > > > # and command not found errors:
> > > > > > > # ensure that mpicxx exists;  ensure that the compiler invoked by
> > > > mpicxx
> > > > > > > exists
> > > > > > > # (for best results it should be g++); in the worst case try manual
> > > > > > linking:
> > > > > > > # change the LOAD definition below to g++, execute the command
> > > > > > > # $MPICH_HOME/bin/mpicc -show
> > > > > > > # and add to the LIBS definition below the output related to link
> > > > flags,
> > > > > > e.g
> > > > > > > # LIBS= -lm -Lyada -Lyada_yada -lbla -lbla_bla ...
> > > > > > > # 2. General advice: build a serial dock first then build a
> > parallel
> > > > > > > # dock using a validated MPI implementation.
> > > > > > > # 3. Best practice advice:  the most straightforward route to
> > > > successful
> > > > > > > # parallel executable building is to use the same compilers for
> > > > building
> > > > > > > # the MPI implementation and dock.
> > > > > > > # END TROUBLESHOOTING
> > > > > > >
> > > > > > > # CC is the C compiler
> > > > > > > # CXX is the C++ compiler
> > > > > > > # CFLAGS is the flags for the C and C++ compilers
> > > > > > > # FC is the Fortran compiler
> > > > > > > # FFLAGS is the flags for the Fortran compiler
> > > > > > > # LIBS is the flags for the linker
> > > > > > > # LOAD is the command to invoke the linker
> > > > > > > # MPICH_IGNORE_CXX_SEEK  see
> > > > > > > #   http://www-unix.mcs.anl.gov/mpi/mpich2/faq.htm#cxxseek
> > > > > > > # MPICH_SKIP_MPICXX  Dock does not use MPI C++ bindings; see
> > > > > > > #
> > > > http://www-unix.mcs.anl.gov/mpi/mpi-standard/mpi-report-2.0/node226.htm
> > > > > > > # SFX is the suffix for the executable
> > > > > > >
> > > > > > > CC=          gcc
> > > > > > > CXX=         g++
> > > > > > > CFLAGS=      -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK
> > > > > > > -DMPICH_SKIP_MPICXX
> > > > > > > -I$(MPICH_HOME)/include -O2
> > > > > > > FC=          g77
> > > > > > > FFLAGS=      -O2 -fno-automatic -fno-second-underscore
> > > > > > > LOAD=        $(MPICH_HOME)/bin/mpicxx
> > > > > > > LIBS=        -lm
> > > > > > > SFX=         .mpi
> > > > > > >
> > > > > > > # Macro definitions for NAB
> > > > > > > # AR is the library archiver
> > > > > > > # LEX is the lexical analyzer generator
> > > > > > > # OCFLAGS is the flags for the C compilers with high optimization
> > > > > > > # RANLIB is the library index generator
> > > > > > > AR=          ar rv
> > > > > > > LEX=         flex
> > > > > > > OCFLAGS=     -O3 -D_ANSI_SOURCE
> > > > > > > RANLIB=      ranlib
> > > > > > > DOCKHOME=/usr/local/dock6
> > > > > > > # Created at Fri Sep 21 18:36:29 CEST 2007 via ./configure gnu
> > parallel
> > > > > > >
> > > > > > >
> > > > > > > I plan to use Antechamber in Amber9.
> > > > > > >
> > > > > > > Thanks
> > > > > > >
> > > > > > > francesco pietra
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
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